This article was created by Dr. Oné Pagán and originally posted on his BaldScientist blog. Reposted with permission.

Molecules are entities composed of at least two atoms, organized in specific ways; they are really small things, and that’s no joke. I would not blame you one bit if you do not “believe” in them, but that makes them no less real, just so you know. Anyway, we all know “in our heads” that everything is made out of atoms and by extension, molecules, but in “our hearts” we find this fact quite mind-boggling and therefore very hard to imagine… Just think about the size of those tiny things!

How small are molecules, really? I could tell you that a hydrogen atom (the simplest atom) is about one Angstrom (Å) wide, but that in itself will not tell you anything. before going into that, let’s talk about how atoms look like in general.


Take again for example, hydrogen. Now, please remember that the usual way that we use to depict atoms, namely the “Solar System” model is far from accurate, but it has been a rather useful working model (see left). This representation is also called the Bohr model, after one of physics great minds, Niels Bohr, who came up with this concept around 1913.

But in reality, electrons are not “orbiting” the nucleus; without going into too much detail, electrons are located “everywhere and nowhere” in a cloud of probability around the nucleus, a little bit like this:

(We also recently took the first picture of this electron cloud, also known as a hydrogen wave function, using a quantum microscope. You can read more about it here.)

Next, think about how big atoms are.  As I said before, I could tell you that a hydrogen atom is about one Angstrom (Å) wide, but that in itself will not help us that much.  Let’s consider the following to try to visualize these size scales.

Basically, this paragraph explained visually. (Credit: BaldScientist)


Then if you take a millimeter and divide it a thousandfold more you get a micrometer (μm); if you take a micrometer and divide it a thousandfold, that’s a nanometer (nM).  Finally, if you take a nanometer and divide it tenfold you get an Angstrom (Ǻ).

Now, I hope that we can all agree that atoms and therefore molecules are tiny, and therefore if we want to see molecules or at the very least take a picture we’d have to use a really powerful microscope, right? Well, a “normal” light microscope or even an electron microscope would not do the trick. We’ll have to use other kind of instruments, like a scanning tunneling microscope (STM) or even better, an atomic force microscope (AFM; which have nothing to do with radioactivity).

Both types of microscopes essentially work by lightly, very lightly “touching” the intended object that we want to image with a really, really fine tip and translating the electron cloud interactions of that tip and the object into a picture. The links at the end of the post will tell you more about these instruments, but what I really want to show you now are examples of what can you see using these kinds of instruments.


Below is a series of pictures showing a particular organic molecule, pentacene, imaged by STM and SFM:

Picture credit: Science 325, 1110 (2009); Leo Gross, et al. The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy.

Don’t the little pentacenes look like little caterpillars?

You have to understand that until very recently, organic chemists deduced the actual structures of molecules through various indirect methods, not by taking pictures of the molecules themselves.  To say that this is a remarkable achievement is a true understatement…

How about chemical reactions?  Well, those have been imaged too!

These types of experiments and techniques have widespread implications, not only for pure chemistry but for structural biology, biochemistry and pharmacology just to start with.  It is truly remarkable to me to think that such small entities like molecules with pharmacological effects are able to interact with not much bigger molecules, like proteins for example and do “their thing”, inducing physiological responses including but not limited to behavior.  In a future post, I hope to explore this a little more.

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